@jbrowse/core 1.5.0 → 1.5.4

package/util/tracks.d.ts

@@ -27,441 +27,38 @@ export declare function storeBlobLocation(location: PreFileLocation): import("./
     blobId: string;
     locationType: string;
 };
-export declare function guessAdapter(file: FileLocation, index: FileLocation | undefined, getFileName: (f: FileLocation) => string, adapterHint?: string): {
-    type: string;
-    bamLocation: FileLocation;
-    index: {
-        location: FileLocation | {
-            uri: string;
-            locationType: string;
-            localPath?: undefined;
-        } | {
-            localPath: string;
-            locationType: string;
-            uri?: undefined;
-        };
-        indexType: string;
-    };
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    cramLocation: FileLocation;
-    craiLocation: FileLocation | {
-        uri: string;
-        locationType: string;
-        localPath?: undefined;
-    } | {
-        localPath: string;
-        locationType: string;
-        uri?: undefined;
-    };
-    bamLocation?: undefined;
-    index?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    gffLocation: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    gffGzLocation: FileLocation;
-    index: {
-        location: FileLocation | {
-            uri: string;
-            locationType: string;
-            localPath?: undefined;
-        } | {
-            localPath: string;
-            locationType: string;
-            uri?: undefined;
-        };
-        indexType: string;
-    };
-    bamLocation?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    vcfLocation: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    vcfGzLocation: FileLocation;
-    index: {
-        location: FileLocation | {
-            uri: string;
-            locationType: string;
-            localPath?: undefined;
-        } | {
-            localPath: string;
-            locationType: string;
-            uri?: undefined;
-        };
-        indexType: string;
-    };
-    bamLocation?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    bedGzLocation: FileLocation;
-    index: {
-        location: FileLocation | {
-            uri: string;
-            locationType: string;
-            localPath?: undefined;
-        } | {
-            localPath: string;
-            locationType: string;
-            uri?: undefined;
-        };
-        indexType: string;
-    };
-    bamLocation?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    bigBedLocation: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    bigWigLocation: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    fastaLocation: FileLocation;
-    faiLocation: FileLocation | {
-        uri: string;
-        locationType: string;
-        localPath?: undefined;
-    } | {
-        localPath: string;
-        locationType: string;
-        uri?: undefined;
-    };
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    fastaLocation: FileLocation;
-    faiLocation: import("./types").BlobLocation | {
-        uri: string;
-        locationType: string;
-        localPath?: undefined;
-    } | {
-        localPath: string;
-        locationType: string;
-        uri?: undefined;
-    };
-    gziLocation: import("./types").BlobLocation | {
-        uri: string;
-        locationType: string;
-        localPath?: undefined;
-    } | {
-        localPath: string;
-        locationType: string;
-        uri?: undefined;
-    };
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    twoBitLocation: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    rootUrlTemplate: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    endpoint: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    hicLocation?: undefined;
-    pafLocation?: undefined;
-} | {
-    type: string;
-    hicLocation: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    pafLocation?: undefined;
+/**
+ * creates a new location from the provided location including the appropriate suffix and location type
+ * @param location - the FileLocation
+ * @param suffix - the file suffix (e.g. .bam)
+ * @returns the constructed location object from the provided prameters
+ */
+export declare function makeIndex(location: FileLocation, suffix: string): import("./types").BlobLocation | {
+    uri: string;
+    locationType: string;
+    localPath?: undefined;
 } | {
-    type: string;
-    pafLocation: FileLocation;
-    bamLocation?: undefined;
-    index?: undefined;
-    cramLocation?: undefined;
-    craiLocation?: undefined;
-    gffLocation?: undefined;
-    gffGzLocation?: undefined;
-    vcfLocation?: undefined;
-    vcfGzLocation?: undefined;
-    bedGzLocation?: undefined;
-    bigBedLocation?: undefined;
-    bigWigLocation?: undefined;
-    fastaLocation?: undefined;
-    faiLocation?: undefined;
-    gziLocation?: undefined;
-    twoBitLocation?: undefined;
-    rootUrlTemplate?: undefined;
-    endpoint?: undefined;
-    hicLocation?: undefined;
+    localPath: string;
+    locationType: string;
+    uri?: undefined;
 };
-export declare function guessTrackType(adapterType: string): string;
+/**
+ * constructs a potential index file (with suffix) from the provided file name
+ * @param name - the name of the index file
+ * @param typeA - one option of a potential two file suffix (e.g. CSI, BAI)
+ * @param typeB - the second option of a potential two file suffix (e.g. CSI, BAI)
+ * @returns a likely name of the index file for a given filename
+ */
+export declare function makeIndexType(name: string | undefined, typeA: string, typeB: string): string;
+export interface AdapterConfig {
+    type: string;
+    [key: string]: unknown;
+}
+export declare type AdapterGuesser = (file: FileLocation, index?: FileLocation, adapterHint?: string) => AdapterConfig | undefined;
+export declare type TrackTypeGuesser = (adapterName: string) => string | undefined;
+export declare function getFileName(track: FileLocation): string;
+export declare function guessAdapter(file: FileLocation, index: FileLocation | undefined, adapterHint?: string, model?: IAnyStateTreeNode): AdapterConfig;
+export declare function guessTrackType(adapterType: string, model?: IAnyStateTreeNode): string;
 export declare function generateUnsupportedTrackConf(trackName: string, trackUrl: string, categories: string[] | undefined): {
     type: string;
     name: string;